We are analyzing how the genomic information orchestrates these events, to discover new principles of organogenesis. Classical models on organ patterning assumed that diffusible morphogens generate a gradient of positional information extra-cellularly. However, cells that have long cellular processes could also exert a long-range effect by localizing molecules to a part of their processes. We found that many membrane proteins are localized to sub-axonal segments even when neurons are isolated from their normal environment in culture. This means that neurons possess an intrinsic mechanism to “pattern” the axon into sub-axonal compartments. By analyzing how such compartments are formed and what they do for the entire nervous system, we aim to build a new framework of organogenesis. The establishment and maintenance of the organ depend on the continual production of cells through the self-renewal division of stem cells. Stem cells acquire their identity through signals from their micro-environment, the niche. Based on our finding that the niche for germline stem cell formation consists of specific somatic cells in the embryonic gonad, we are studying the molecular identity of the niche signal.